Are we talking about the battle system or the stat/ability system?

If we're talking about the battle system, I go with X-2. It was just real fun, insane, and awesome. I loved being able to switch classes and have practically a whole different character in mid battle.

If we're talking about stat/ability system, I go with VII's Materia system, mainly because Materia was a real big part of the story and tied in so well.